Merge pull request #5 from jorizci/EE-504

EE-504 accessioning alpha application

.gitignore

@@ -0,0 +1,20 @@
+*.class
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.ear
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+
+# IntelliJ files
+*.iml
+.idea
+
+# Maven target directory
+target
+/.project

pom.xml

@@ -24,8 +24,13 @@
     <dependencies>
         <dependency>
             <groupId>uk.ac.ebi.ampt2d</groupId>
-            <artifactId>accessioning-commons</artifactId>
-            <version>1.0-SNAPSHOT</version>
+            <artifactId>accession-commons-jpa</artifactId>
+            <version>0.6-SNAPSHOT</version>
+        </dependency>
+        <dependency>
+            <groupId>uk.ac.ebi.ampt2d</groupId>
+            <artifactId>accession-commons-monotonic-generator-jpa</artifactId>
+            <version>0.6-SNAPSHOT</version>
         </dependency>
 
         <dependency>

src/main/java/uk/ac/ebi/ega/accession/EGAAccessioningApplication.java → src/main/java/uk/ac/ebi/ega/accession/EgaAccessioningApplication.java

@@ -23,14 +23,14 @@
 import org.springframework.boot.web.support.SpringBootServletInitializer;
 
 @SpringBootApplication
-public class EGAAccessioningApplication extends SpringBootServletInitializer {
+public class EgaAccessioningApplication extends SpringBootServletInitializer {
 
     @Override
     protected SpringApplicationBuilder configure(SpringApplicationBuilder application) {
-        return application.sources(EGAAccessioningApplication.class);
+        return application.sources(EgaAccessioningApplication.class);
     }
 
-    public static void main(String[] args) throws Exception {
-        SpringApplication.run(EGAAccessioningApplication.class, args);
+    public static void main(String[] args) {
+        SpringApplication.run(EgaAccessioningApplication.class, args);
     }
 }

src/main/java/uk/ac/ebi/ega/accession/study/StudyModel.java → src/main/java/uk/ac/ebi/ega/accession/analysis/model/Analysis.java

@@ -15,11 +15,12 @@
  * limitations under the License.
  *
  */
+package uk.ac.ebi.ega.accession.analysis.model;
 
-package uk.ac.ebi.ega.accession.study;
+public interface Analysis {
 
-import java.util.Map;
+    String getSubmissionAccount();
+
+    String getAlias();
 
-public interface StudyModel {
-    Map<String, String> getStudyProperties();
 }

src/main/java/uk/ac/ebi/ega/accession/analysis/persistence/AnalysisEntity.java

@@ -0,0 +1,64 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ega.accession.analysis.persistence;
+
+import uk.ac.ebi.ampt2d.commons.accession.core.models.AccessionWrapper;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.AccessionedEntity;
+import uk.ac.ebi.ega.accession.analysis.model.Analysis;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+
+@Entity
+public class AnalysisEntity extends AccessionedEntity<Analysis, Long> implements Analysis {
+
+    @Column(nullable = false)
+    private String submissionAccount;
+
+    @Column(nullable = false)
+    private String alias;
+
+    AnalysisEntity() {
+        super(null, null, -1);
+    }
+
+    public AnalysisEntity(Analysis analysis, Long accession, String hashedMessage, int version) {
+        super(hashedMessage, accession, version);
+        this.submissionAccount = analysis.getSubmissionAccount();
+        this.alias = analysis.getAlias();
+    }
+
+    public AnalysisEntity(AccessionWrapper<Analysis, String, Long> wrapper) {
+        this(wrapper.getData(), wrapper.getAccession(), wrapper.getHash(), wrapper.getVersion());
+    }
+
+    @Override
+    public Analysis getModel() {
+        return this;
+    }
+
+    @Override
+    public String getSubmissionAccount() {
+        return submissionAccount;
+    }
+
+    @Override
+    public String getAlias() {
+        return alias;
+    }
+}

src/main/java/uk/ac/ebi/ega/accession/analysis/persistence/AnalysisEntityRepository.java

@@ -0,0 +1,26 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ega.accession.analysis.persistence;
+
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.repositories.IAccessionedObjectRepository;
+
+@Repository
+public interface AnalysisEntityRepository extends IAccessionedObjectRepository<AnalysisEntity, Long> {
+
+}

src/main/java/uk/ac/ebi/ega/accession/analysis/persistence/AnalysisEntityRepositoryImpl.java

@@ -0,0 +1,30 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ega.accession.analysis.persistence;
+
+import org.springframework.transaction.PlatformTransactionManager;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.repositories.BasicJpaAccessionedObjectCustomRepositoryImpl;
+
+import javax.persistence.EntityManager;
+
+public class AnalysisEntityRepositoryImpl extends BasicJpaAccessionedObjectCustomRepositoryImpl<Long, AnalysisEntity> {
+
+    public AnalysisEntityRepositoryImpl(PlatformTransactionManager platformTransactionManager, EntityManager entityManager) {
+        super(AnalysisEntity.class, platformTransactionManager, entityManager);
+    }
+}

src/main/java/uk/ac/ebi/ega/accession/analysis/persistence/HistoricAnalysisEntity.java

@@ -0,0 +1,59 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ega.accession.analysis.persistence;
+
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.InactiveAccessionEntity;
+import uk.ac.ebi.ega.accession.analysis.model.Analysis;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+
+@Entity
+public class HistoricAnalysisEntity extends InactiveAccessionEntity<Analysis, Long> implements Analysis {
+
+    @Column(nullable = false)
+    private String submissionAccount;
+
+    @Column(nullable = false)
+    private String alias;
+
+    HistoricAnalysisEntity() {
+        super();
+    }
+
+    public HistoricAnalysisEntity(AnalysisEntity entity) {
+        super(entity);
+        this.submissionAccount = entity.getSubmissionAccount();
+        this.alias = entity.getAlias();
+    }
+
+    @Override
+    public Analysis getModel() {
+        return this;
+    }
+
+    @Override
+    public String getSubmissionAccount() {
+        return submissionAccount;
+    }
+
+    @Override
+    public String getAlias() {
+        return alias;
+    }
+}

src/main/java/uk/ac/ebi/ega/accession/analysis/persistence/HistoricAnalysisRepository.java

@@ -0,0 +1,26 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ega.accession.analysis.persistence;
+
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.repositories.InactiveAccessionRepository;
+
+@Repository
+public interface HistoricAnalysisRepository extends InactiveAccessionRepository<HistoricAnalysisEntity> {
+
+}

src/main/java/uk/ac/ebi/ega/accession/analysis/persistence/HistoricLogAnalysisEntity.java

@@ -0,0 +1,26 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ega.accession.analysis.persistence;
+
+import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.entities.OperationEntity;
+
+import javax.persistence.Entity;
+
+@Entity
+public class HistoricLogAnalysisEntity extends OperationEntity<Long> {
+}

src/main/java/uk/ac/ebi/ega/accession/analysis/persistence/HistoricLogAnalysisRepository.java

@@ -0,0 +1,26 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ega.accession.analysis.persistence;
+
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.ampt2d.commons.accession.persistence.repositories.IHistoryRepository;
+
+@Repository
+public interface HistoricLogAnalysisRepository extends IHistoryRepository<Long, HistoricLogAnalysisEntity, Long> {
+
+}

src/main/java/uk/ac/ebi/ega/accession/analysis/rest/AnalysisDTO.java

@@ -0,0 +1,54 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ega.accession.analysis.rest;
+
+import uk.ac.ebi.ega.accession.analysis.model.Analysis;
+
+import javax.persistence.Column;
+
+public class AnalysisDTO implements Analysis {
+
+    @Column(nullable = false)
+    private String submissionAccount;
+
+    @Column(nullable = false)
+    private String alias;
+
+    AnalysisDTO(){
+    }
+
+    public AnalysisDTO(Analysis analysis) {
+        this(analysis.getSubmissionAccount(), analysis.getAlias());
+    }
+
+    public AnalysisDTO(String submissionAccount, String alias) {
+        this.submissionAccount = submissionAccount;
+        this.alias = alias;
+    }
+
+    @Override
+    public String getSubmissionAccount() {
+        return submissionAccount;
+    }
+
+    @Override
+    public String getAlias() {
+        return alias;
+    }
+
+}